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root/OpenMD/branches/devel_omp/src/brains/ForceManager.cpp

Comparing branches/devel_omp/src/brains/ForceManager.cpp (file contents):
Revision 1597 by chuckv, Tue Jul 19 18:50:04 2011 UTC vs.
Revision 1598 by mciznick, Wed Jul 27 14:26:53 2011 UTC

#	Line 38 | Line 38
38		* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39		* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41	<
41	>
42		/**
43		* @file ForceManager.cpp
44		* @author tlin
#	Line 47 | Line 47
47		* @version 1.0
48		*/
49
50	–
50		#include "brains/ForceManager.hpp"
51		#include "primitives/Molecule.hpp"
52		#define __OPENMD_C
#	Line 63 | Line 62
62		#include <iostream>
63		#include <iomanip>
64
65	+	#include <omp.h>
66	+
67		using namespace std;
68		namespace OpenMD {
68	–
69	–	ForceManager::ForceManager(SimInfo * info) : info_(info) {
70	–	forceField_ = info_->getForceField();
71	–	interactionMan_ = new InteractionManager();
72	–	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
73	–	}
69
70	<	/**
71	<	* setupCutoffs
72	<	*
73	<	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
74	<	* and cutoffPolicy
75	<	*
81	<	* cutoffRadius : realType
82	<	*  If the cutoffRadius was explicitly set, use that value.
83	<	*  If the cutoffRadius was not explicitly set:
84	<	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
85	<	*      No electrostatic atoms?  Poll the atom types present in the
86	<	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
87	<	*      Use the maximum suggested value that was found.
88	<	*
89	<	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
90	<	*                        or SHIFTED_POTENTIAL)
91	<	*      If cutoffMethod was explicitly set, use that choice.
92	<	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
93	<	*
94	<	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
95	<	*      If cutoffPolicy was explicitly set, use that choice.
96	<	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
97	<	*
98	<	* switchingRadius : realType
99	<	*  If the cutoffMethod was set to SWITCHED:
100	<	*      If the switchingRadius was explicitly set, use that value
101	<	*          (but do a sanity check first).
102	<	*      If the switchingRadius was not explicitly set: use 0.85 *
103	<	*      cutoffRadius_
104	<	*  If the cutoffMethod was not set to SWITCHED:
105	<	*      Set switchingRadius equal to cutoffRadius for safety.
106	<	*/
107	<	void ForceManager::setupCutoffs() {
108	<
109	<	Globals* simParams_ = info_->getSimParams();
110	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
111	<
112	<	if (simParams_->haveCutoffRadius()) {
113	<	rCut_ = simParams_->getCutoffRadius();
114	<	} else {
115	<	if (info_->usesElectrostaticAtoms()) {
116	<	sprintf(painCave.errMsg,
117	<	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
118	<	"\tOpenMD will use a default value of 12.0 angstroms"
119	<	"\tfor the cutoffRadius.\n");
120	<	painCave.isFatal = 0;
121	<	painCave.severity = OPENMD_INFO;
122	<	simError();
123	<	rCut_ = 12.0;
124	<	} else {
125	<	RealType thisCut;
126	<	set<AtomType*>::iterator i;
127	<	set<AtomType*> atomTypes;
128	<	atomTypes = info_->getSimulatedAtomTypes();
129	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
130	<	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
131	<	rCut_ = max(thisCut, rCut_);
132	<	}
133	<	sprintf(painCave.errMsg,
134	<	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
135	<	"\tOpenMD will use %lf angstroms.\n",
136	<	rCut_);
137	<	painCave.isFatal = 0;
138	<	painCave.severity = OPENMD_INFO;
139	<	simError();
140	<	}
141	<	}
70	>	ForceManager::ForceManager(SimInfo * info) :
71	>	info_(info) {
72	>	forceField_ = info_->getForceField();
73	>	interactionMan_ = new InteractionManager();
74	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
75	>	}
76
77	<	fDecomp_->setUserCutoff(rCut_);
78	<	interactionMan_->setCutoffRadius(rCut_);
77	>	/**
78	>	* setupCutoffs
79	>	*
80	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
81	>	* and cutoffPolicy
82	>	*
83	>	* cutoffRadius : realType
84	>	*  If the cutoffRadius was explicitly set, use that value.
85	>	*  If the cutoffRadius was not explicitly set:
86	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
87	>	*      No electrostatic atoms?  Poll the atom types present in the
88	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
89	>	*      Use the maximum suggested value that was found.
90	>	*
91	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
92	>	*                        or SHIFTED_POTENTIAL)
93	>	*      If cutoffMethod was explicitly set, use that choice.
94	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
95	>	*
96	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
97	>	*      If cutoffPolicy was explicitly set, use that choice.
98	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
99	>	*
100	>	* switchingRadius : realType
101	>	*  If the cutoffMethod was set to SWITCHED:
102	>	*      If the switchingRadius was explicitly set, use that value
103	>	*          (but do a sanity check first).
104	>	*      If the switchingRadius was not explicitly set: use 0.85 *
105	>	*      cutoffRadius_
106	>	*  If the cutoffMethod was not set to SWITCHED:
107	>	*      Set switchingRadius equal to cutoffRadius for safety.
108	>	*/
109	>	void ForceManager::setupCutoffs() {
110
111	<	map<string, CutoffMethod> stringToCutoffMethod;
112	<	stringToCutoffMethod["HARD"] = HARD;
148	<	stringToCutoffMethod["SWITCHED"] = SWITCHED;
149	<	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
150	<	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
151	<
152	<	if (simParams_->haveCutoffMethod()) {
153	<	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
154	<	map<string, CutoffMethod>::iterator i;
155	<	i = stringToCutoffMethod.find(cutMeth);
156	<	if (i == stringToCutoffMethod.end()) {
157	<	sprintf(painCave.errMsg,
158	<	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
159	<	"\tShould be one of: "
160	<	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
161	<	cutMeth.c_str());
162	<	painCave.isFatal = 1;
163	<	painCave.severity = OPENMD_ERROR;
164	<	simError();
165	<	} else {
166	<	cutoffMethod_ = i->second;
167	<	}
168	<	} else {
169	<	sprintf(painCave.errMsg,
170	<	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
171	<	"\tOpenMD will use SHIFTED_FORCE.\n");
172	<	painCave.isFatal = 0;
173	<	painCave.severity = OPENMD_INFO;
174	<	simError();
175	<	cutoffMethod_ = SHIFTED_FORCE;
176	<	}
111	>	Globals* simParams_ = info_->getSimParams();
112	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
113
114	<	map<string, CutoffPolicy> stringToCutoffPolicy;
115	<	stringToCutoffPolicy["MIX"] = MIX;
116	<	stringToCutoffPolicy["MAX"] = MAX;
117	<	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
114	>	if (simParams_->haveCutoffRadius())
115	>	{
116	>	rCut_ = simParams_->getCutoffRadius();
117	>	} else
118	>	{
119	>	if (info_->usesElectrostaticAtoms())
120	>	{
121	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
122	>	"\tOpenMD will use a default value of 12.0 angstroms"
123	>	"\tfor the cutoffRadius.\n");
124	>	painCave.isFatal = 0;
125	>	painCave.severity = OPENMD_INFO;
126	>	simError();
127	>	rCut_ = 12.0;
128	>	} else
129	>	{
130	>	RealType thisCut;
131	>	set<AtomType*>::iterator i;
132	>	set<AtomType*> atomTypes;
133	>	atomTypes = info_->getSimulatedAtomTypes();
134	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
135	>	{
136	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
137	>	rCut_ = max(thisCut, rCut_);
138	>	}
139	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
140	>	"\tOpenMD will use %lf angstroms.\n", rCut_);
141	>	painCave.isFatal = 0;
142	>	painCave.severity = OPENMD_INFO;
143	>	simError();
144	>	}
145	>	}
146
147	<	std::string cutPolicy;
148	<	if (forceFieldOptions_.haveCutoffPolicy()){
185	<	cutPolicy = forceFieldOptions_.getCutoffPolicy();
186	<	}else if (simParams_->haveCutoffPolicy()) {
187	<	cutPolicy = simParams_->getCutoffPolicy();
188	<	}
147	>	fDecomp_->setUserCutoff(rCut_);
148	>	interactionMan_->setCutoffRadius(rCut_);
149
150	<	if (!cutPolicy.empty()){
151	<	toUpper(cutPolicy);
152	<	map<string, CutoffPolicy>::iterator i;
153	<	i = stringToCutoffPolicy.find(cutPolicy);
150	>	map<string, CutoffMethod> stringToCutoffMethod;
151	>	stringToCutoffMethod["HARD"] = HARD;
152	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
153	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
154	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
155
156	<	if (i == stringToCutoffPolicy.end()) {
157	<	sprintf(painCave.errMsg,
158	<	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
159	<	"\tShould be one of: "
160	<	"MIX, MAX, or TRADITIONAL\n",
161	<	cutPolicy.c_str());
162	<	painCave.isFatal = 1;
163	<	painCave.severity = OPENMD_ERROR;
164	<	simError();
165	<	} else {
166	<	cutoffPolicy_ = i->second;
167	<	}
168	<	} else {
169	<	sprintf(painCave.errMsg,
170	<	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
171	<	"\tOpenMD will use TRADITIONAL.\n");
172	<	painCave.isFatal = 0;
173	<	painCave.severity = OPENMD_INFO;
174	<	simError();
175	<	cutoffPolicy_ = TRADITIONAL;
176	<	}
156	>	if (simParams_->haveCutoffMethod())
157	>	{
158	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
159	>	map<string, CutoffMethod>::iterator i;
160	>	i = stringToCutoffMethod.find(cutMeth);
161	>	if (i == stringToCutoffMethod.end())
162	>	{
163	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
164	>	"\tShould be one of: "
165	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n", cutMeth.c_str());
166	>	painCave.isFatal = 1;
167	>	painCave.severity = OPENMD_ERROR;
168	>	simError();
169	>	} else
170	>	{
171	>	cutoffMethod_ = i->second;
172	>	}
173	>	} else
174	>	{
175	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
176	>	"\tOpenMD will use SHIFTED_FORCE.\n");
177	>	painCave.isFatal = 0;
178	>	painCave.severity = OPENMD_INFO;
179	>	simError();
180	>	cutoffMethod_ = SHIFTED_FORCE;
181	>	}
182
183	<	fDecomp_->setCutoffPolicy(cutoffPolicy_);
184	<
185	<	// create the switching function object:
183	>	map<string, CutoffPolicy> stringToCutoffPolicy;
184	>	stringToCutoffPolicy["MIX"] = MIX;
185	>	stringToCutoffPolicy["MAX"] = MAX;
186	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
187
188	<	switcher_ = new SwitchingFunction();
189	<
190	<	if (cutoffMethod_ == SWITCHED) {
191	<	if (simParams_->haveSwitchingRadius()) {
192	<	rSwitch_ = simParams_->getSwitchingRadius();
193	<	if (rSwitch_ > rCut_) {
194	<	sprintf(painCave.errMsg,
195	<	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
229	<	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
230	<	painCave.isFatal = 1;
231	<	painCave.severity = OPENMD_ERROR;
232	<	simError();
233	<	}
234	<	} else {
235	<	rSwitch_ = 0.85 * rCut_;
236	<	sprintf(painCave.errMsg,
237	<	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
238	<	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
239	<	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
240	<	painCave.isFatal = 0;
241	<	painCave.severity = OPENMD_WARNING;
242	<	simError();
243	<	}
244	<	} else {
245	<	if (simParams_->haveSwitchingRadius()) {
246	<	map<string, CutoffMethod>::const_iterator it;
247	<	string theMeth;
248	<	for (it = stringToCutoffMethod.begin();
249	<	it != stringToCutoffMethod.end(); ++it) {
250	<	if (it->second == cutoffMethod_) {
251	<	theMeth = it->first;
252	<	break;
253	<	}
254	<	}
255	<	sprintf(painCave.errMsg,
256	<	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
257	<	"\tis not set to SWITCHED, so switchingRadius value\n"
258	<	"\twill be ignored for this simulation\n", theMeth.c_str());
259	<	painCave.isFatal = 0;
260	<	painCave.severity = OPENMD_WARNING;
261	<	simError();
262	<	}
188	>	std::string cutPolicy;
189	>	if (forceFieldOptions_.haveCutoffPolicy())
190	>	{
191	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
192	>	} else if (simParams_->haveCutoffPolicy())
193	>	{
194	>	cutPolicy = simParams_->getCutoffPolicy();
195	>	}
196
197	<	rSwitch_ = rCut_;
198	<	}
199	<
200	<	// Default to cubic switching function.
201	<	sft_ = cubic;
269	<	if (simParams_->haveSwitchingFunctionType()) {
270	<	string funcType = simParams_->getSwitchingFunctionType();
271	<	toUpper(funcType);
272	<	if (funcType == "CUBIC") {
273	<	sft_ = cubic;
274	<	} else {
275	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
276	<	sft_ = fifth_order_poly;
277	<	} else {
278	<	// throw error
279	<	sprintf( painCave.errMsg,
280	<	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
281	<	"\tswitchingFunctionType must be one of: "
282	<	"\"cubic\" or \"fifth_order_polynomial\".",
283	<	funcType.c_str() );
284	<	painCave.isFatal = 1;
285	<	painCave.severity = OPENMD_ERROR;
286	<	simError();
287	<	}
288	<	}
289	<	}
290	<	switcher_->setSwitchType(sft_);
291	<	switcher_->setSwitch(rSwitch_, rCut_);
292	<	interactionMan_->setSwitchingRadius(rSwitch_);
293	<	}
294	<
295	<	void ForceManager::initialize() {
197	>	if (!cutPolicy.empty())
198	>	{
199	>	toUpper(cutPolicy);
200	>	map<string, CutoffPolicy>::iterator i;
201	>	i = stringToCutoffPolicy.find(cutPolicy);
202
203	<	if (!info_->isTopologyDone()) {
203	>	if (i == stringToCutoffPolicy.end())
204	>	{
205	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
206	>	"\tShould be one of: "
207	>	"MIX, MAX, or TRADITIONAL\n", cutPolicy.c_str());
208	>	painCave.isFatal = 1;
209	>	painCave.severity = OPENMD_ERROR;
210	>	simError();
211	>	} else
212	>	{
213	>	cutoffPolicy_ = i->second;
214	>	}
215	>	} else
216	>	{
217	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
218	>	"\tOpenMD will use TRADITIONAL.\n");
219	>	painCave.isFatal = 0;
220	>	painCave.severity = OPENMD_INFO;
221	>	simError();
222	>	cutoffPolicy_ = TRADITIONAL;
223	>	}
224
225	<	info_->update();
300	<	interactionMan_->setSimInfo(info_);
301	<	interactionMan_->initialize();
225	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
226
227	<	// We want to delay the cutoffs until after the interaction
304	<	// manager has set up the atom-atom interactions so that we can
305	<	// query them for suggested cutoff values
306	<	setupCutoffs();
227	>	// create the switching function object:
228
229	<	info_->prepareTopology();
309	<	}
229	>	switcher_ = new SwitchingFunction();
230
231	<	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
232	<
233	<	// Force fields can set options on how to scale van der Waals and
234	<	// electrostatic interactions for atoms connected via bonds, bends
235	<	// and torsions in this case the topological distance between
236	<	// atoms is:
237	<	// 0 = topologically unconnected
238	<	// 1 = bonded together
239	<	// 2 = connected via a bend
240	<	// 3 = connected via a torsion
241	<
242	<	vdwScale_.reserve(4);
243	<	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
231	>	if (cutoffMethod_ == SWITCHED)
232	>	{
233	>	if (simParams_->haveSwitchingRadius())
234	>	{
235	>	rSwitch_ = simParams_->getSwitchingRadius();
236	>	if (rSwitch_ > rCut_)
237	>	{
238	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
239	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
240	>	painCave.isFatal = 1;
241	>	painCave.severity = OPENMD_ERROR;
242	>	simError();
243	>	}
244	>	} else
245	>	{
246	>	rSwitch_ = 0.85 * rCut_;
247	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
248	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
249	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
250	>	painCave.isFatal = 0;
251	>	painCave.severity = OPENMD_WARNING;
252	>	simError();
253	>	}
254	>	} else
255	>	{
256	>	if (simParams_->haveSwitchingRadius())
257	>	{
258	>	map<string, CutoffMethod>::const_iterator it;
259	>	string theMeth;
260	>	for (it = stringToCutoffMethod.begin(); it != stringToCutoffMethod.end(); ++it)
261	>	{
262	>	if (it->second == cutoffMethod_)
263	>	{
264	>	theMeth = it->first;
265	>	break;
266	>	}
267	>	}
268	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
269	>	"\tis not set to SWITCHED, so switchingRadius value\n"
270	>	"\twill be ignored for this simulation\n", theMeth.c_str());
271	>	painCave.isFatal = 0;
272	>	painCave.severity = OPENMD_WARNING;
273	>	simError();
274	>	}
275
276	<	electrostaticScale_.reserve(4);
277	<	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
276	>	rSwitch_ = rCut_;
277	>	}
278
279	<	vdwScale_[0] = 1.0;
280	<	vdwScale_[1] = fopts.getvdw12scale();
281	<	vdwScale_[2] = fopts.getvdw13scale();
282	<	vdwScale_[3] = fopts.getvdw14scale();
283	<
284	<	electrostaticScale_[0] = 1.0;
285	<	electrostaticScale_[1] = fopts.getelectrostatic12scale();
286	<	electrostaticScale_[2] = fopts.getelectrostatic13scale();
287	<	electrostaticScale_[3] = fopts.getelectrostatic14scale();
288	<
289	<	fDecomp_->distributeInitialData();
290	<
291	<	initialized_ = true;
279	>	// Default to cubic switching function.
280	>	sft_ = cubic;
281	>	if (simParams_->haveSwitchingFunctionType())
282	>	{
283	>	string funcType = simParams_->getSwitchingFunctionType();
284	>	toUpper(funcType);
285	>	if (funcType == "CUBIC")
286	>	{
287	>	sft_ = cubic;
288	>	} else
289	>	{
290	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL")
291	>	{
292	>	sft_ = fifth_order_poly;
293	>	} else
294	>	{
295	>	// throw error
296	>	sprintf(painCave.errMsg,
297	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
298	>	"\tswitchingFunctionType must be one of: "
299	>	"\"cubic\" or \"fifth_order_polynomial\".", funcType.c_str());
300	>	painCave.isFatal = 1;
301	>	painCave.severity = OPENMD_ERROR;
302	>	simError();
303	>	}
304	>	}
305	>	}
306	>	switcher_->setSwitchType(sft_);
307	>	switcher_->setSwitch(rSwitch_, rCut_);
308	>	interactionMan_->setSwitchingRadius(rSwitch_);
309	>	}
310
311	<	}
311	>	void ForceManager::initialize() {
312
313	<	void ForceManager::calcForces() {
314	<
346	<	if (!initialized_) initialize();
313	>	if (!info_->isTopologyDone())
314	>	{
315
316	<	preCalculation();
317	<	shortRangeInteractions();
318	<	//    longRangeInteractions();
351	<	longRangeInteractionsRapaport();
352	<	postCalculation();
353	<	}
354	<
355	<	void ForceManager::preCalculation() {
356	<	SimInfo::MoleculeIterator mi;
357	<	Molecule* mol;
358	<	Molecule::AtomIterator ai;
359	<	Atom* atom;
360	<	Molecule::RigidBodyIterator rbIter;
361	<	RigidBody* rb;
362	<	Molecule::CutoffGroupIterator ci;
363	<	CutoffGroup* cg;
364	<
365	<	// forces are zeroed here, before any are accumulated.
366	<
367	<	for (mol = info_->beginMolecule(mi); mol != NULL;
368	<	mol = info_->nextMolecule(mi)) {
369	<	for(atom = mol->beginAtom(ai); atom != NULL;
370	<	atom = mol->nextAtom(ai)) {
371	<	atom->zeroForcesAndTorques();
372	<	}
373	<
374	<	//change the positions of atoms which belong to the rigidbodies
375	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
376	<	rb = mol->nextRigidBody(rbIter)) {
377	<	rb->zeroForcesAndTorques();
378	<	}
379	<
380	<	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
381	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
382	<	cg = mol->nextCutoffGroup(ci)) {
383	<	//calculate the center of mass of cutoff group
384	<	cg->updateCOM();
385	<	}
386	<	}
387	<	}
388	<
389	<	// Zero out the stress tensor
390	<	tau *= 0.0;
391	<
392	<	}
393	<
394	<	void ForceManager::shortRangeInteractions() {
395	<	Molecule* mol;
396	<	RigidBody* rb;
397	<	Bond* bond;
398	<	Bend* bend;
399	<	Torsion* torsion;
400	<	Inversion* inversion;
401	<	SimInfo::MoleculeIterator mi;
402	<	Molecule::RigidBodyIterator rbIter;
403	<	Molecule::BondIterator bondIter;;
404	<	Molecule::BendIterator  bendIter;
405	<	Molecule::TorsionIterator  torsionIter;
406	<	Molecule::InversionIterator  inversionIter;
407	<	RealType bondPotential = 0.0;
408	<	RealType bendPotential = 0.0;
409	<	RealType torsionPotential = 0.0;
410	<	RealType inversionPotential = 0.0;
316	>	info_->update();
317	>	interactionMan_->setSimInfo(info_);
318	>	interactionMan_->initialize();
319
320	<	//calculate short range interactions
321	<	for (mol = info_->beginMolecule(mi); mol != NULL;
322	<	mol = info_->nextMolecule(mi)) {
320	>	// We want to delay the cutoffs until after the interaction
321	>	// manager has set up the atom-atom interactions so that we can
322	>	// query them for suggested cutoff values
323	>	setupCutoffs();
324
325	<	//change the positions of atoms which belong to the rigidbodies
326	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
418	<	rb = mol->nextRigidBody(rbIter)) {
419	<	rb->updateAtoms();
420	<	}
325	>	info_->prepareTopology();
326	>	}
327
328	<	for (bond = mol->beginBond(bondIter); bond != NULL;
423	<	bond = mol->nextBond(bondIter)) {
424	<	bond->calcForce();
425	<	bondPotential += bond->getPotential();
426	<	}
328	>	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
329
330	<	for (bend = mol->beginBend(bendIter); bend != NULL;
331	<	bend = mol->nextBend(bendIter)) {
332	<
333	<	RealType angle;
334	<	bend->calcForce(angle);
335	<	RealType currBendPot = bend->getPotential();
336	<
337	<	bendPotential += bend->getPotential();
436	<	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
437	<	if (i == bendDataSets.end()) {
438	<	BendDataSet dataSet;
439	<	dataSet.prev.angle = dataSet.curr.angle = angle;
440	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
441	<	dataSet.deltaV = 0.0;
442	<	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
443	<	dataSet));
444	<	}else {
445	<	i->second.prev.angle = i->second.curr.angle;
446	<	i->second.prev.potential = i->second.curr.potential;
447	<	i->second.curr.angle = angle;
448	<	i->second.curr.potential = currBendPot;
449	<	i->second.deltaV =  fabs(i->second.curr.potential -
450	<	i->second.prev.potential);
451	<	}
452	<	}
453	<
454	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
455	<	torsion = mol->nextTorsion(torsionIter)) {
456	<	RealType angle;
457	<	torsion->calcForce(angle);
458	<	RealType currTorsionPot = torsion->getPotential();
459	<	torsionPotential += torsion->getPotential();
460	<	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
461	<	if (i == torsionDataSets.end()) {
462	<	TorsionDataSet dataSet;
463	<	dataSet.prev.angle = dataSet.curr.angle = angle;
464	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
465	<	dataSet.deltaV = 0.0;
466	<	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
467	<	}else {
468	<	i->second.prev.angle = i->second.curr.angle;
469	<	i->second.prev.potential = i->second.curr.potential;
470	<	i->second.curr.angle = angle;
471	<	i->second.curr.potential = currTorsionPot;
472	<	i->second.deltaV =  fabs(i->second.curr.potential -
473	<	i->second.prev.potential);
474	<	}
475	<	}
476	<
477	<	for (inversion = mol->beginInversion(inversionIter);
478	<	inversion != NULL;
479	<	inversion = mol->nextInversion(inversionIter)) {
480	<	RealType angle;
481	<	inversion->calcForce(angle);
482	<	RealType currInversionPot = inversion->getPotential();
483	<	inversionPotential += inversion->getPotential();
484	<	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
485	<	if (i == inversionDataSets.end()) {
486	<	InversionDataSet dataSet;
487	<	dataSet.prev.angle = dataSet.curr.angle = angle;
488	<	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
489	<	dataSet.deltaV = 0.0;
490	<	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
491	<	}else {
492	<	i->second.prev.angle = i->second.curr.angle;
493	<	i->second.prev.potential = i->second.curr.potential;
494	<	i->second.curr.angle = angle;
495	<	i->second.curr.potential = currInversionPot;
496	<	i->second.deltaV =  fabs(i->second.curr.potential -
497	<	i->second.prev.potential);
498	<	}
499	<	}
500	<	}
501	<
502	<	RealType  shortRangePotential = bondPotential + bendPotential +
503	<	torsionPotential +  inversionPotential;
504	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
505	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
506	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
507	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
508	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
509	<	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
510	<	}
511	<
512	<	void ForceManager::longRangeInteractionsRapaport() {
330	>	// Force fields can set options on how to scale van der Waals and
331	>	// electrostatic interactions for atoms connected via bonds, bends
332	>	// and torsions in this case the topological distance between
333	>	// atoms is:
334	>	// 0 = topologically unconnected
335	>	// 1 = bonded together
336	>	// 2 = connected via a bend
337	>	// 3 = connected via a torsion
338
339	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
340	<	DataStorage* config = &(curSnapshot->atomData);
516	<	DataStorage* cgConfig = &(curSnapshot->cgData);
339	>	vdwScale_.reserve(4);
340	>	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
341
342	<	//calculate the center of mass of cutoff group
342	>	electrostaticScale_.reserve(4);
343	>	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
344
345	<	SimInfo::MoleculeIterator mi;
346	<	Molecule* mol;
347	<	Molecule::CutoffGroupIterator ci;
348	<	CutoffGroup* cg;
345	>	vdwScale_[0] = 1.0;
346	>	vdwScale_[1] = fopts.getvdw12scale();
347	>	vdwScale_[2] = fopts.getvdw13scale();
348	>	vdwScale_[3] = fopts.getvdw14scale();
349
350	<	if(info_->getNCutoffGroups() > 0){
351	<	for (mol = info_->beginMolecule(mi); mol != NULL;
352	<	mol = info_->nextMolecule(mi)) {
353	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
529	<	cg = mol->nextCutoffGroup(ci)) {
530	<	cerr << "branch1\n";
531	<	cerr << "globind = " << cg->getGlobalIndex() << "\n";
532	<	cg->updateCOM();
533	<	}
534	<	}
535	<	} else {
536	<	// center of mass of the group is the same as position of the atom
537	<	// if cutoff group does not exist
538	<	cerr << "branch2\n";
539	<	cgConfig->position = config->position;
540	<	}
350	>	electrostaticScale_[0] = 1.0;
351	>	electrostaticScale_[1] = fopts.getelectrostatic12scale();
352	>	electrostaticScale_[2] = fopts.getelectrostatic13scale();
353	>	electrostaticScale_[3] = fopts.getelectrostatic14scale();
354
355	<	fDecomp_->zeroWorkArrays();
543	<	fDecomp_->distributeData();
355	>	fDecomp_->distributeInitialData();
356
357	<	int cg1, cg2, atom1, atom2, topoDist;
546	<	Vector3d d_grp, dag, d;
547	<	RealType rgrpsq, rgrp, r2, r;
548	<	RealType electroMult, vdwMult;
549	<	RealType vij;
550	<	Vector3d fij, fg, f1;
551	<	tuple3<RealType, RealType, RealType> cuts;
552	<	RealType rCutSq;
553	<	bool in_switching_region;
554	<	RealType sw, dswdr, swderiv;
555	<	vector<int> atomListColumn, atomListRow, atomListLocal;
556	<	InteractionData idat;
557	<	SelfData sdat;
558	<	RealType mf;
559	<	RealType lrPot;
560	<	RealType vpair;
561	<	potVec longRangePotential(0.0);
562	<	potVec workPot(0.0);
357	>	initialized_ = true;
358
359	<	int loopStart, loopEnd;
359	>	}
360
361	<	idat.vdwMult = &vdwMult;
567	<	idat.electroMult = &electroMult;
568	<	idat.pot = &workPot;
569	<	sdat.pot = fDecomp_->getEmbeddingPotential();
570	<	idat.vpair = &vpair;
571	<	idat.f1 = &f1;
572	<	idat.sw = &sw;
573	<	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
574	<	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
361	>	void ForceManager::calcForces() {
362
363	<	loopEnd = PAIR_LOOP;
364	<	if (info_->requiresPrepair() ) {
578	<	loopStart = PREPAIR_LOOP;
579	<	} else {
580	<	loopStart = PAIR_LOOP;
581	<	}
363	>	if (!initialized_)
364	>	initialize();
365
366	<	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
366	>	preCalculation();
367	>	shortRangeInteractions();
368	>	//    longRangeInteractions();
369	>	longRangeInteractionsRapaport();
370	>	postCalculation();
371	>	}
372
373	<	if (iLoop == loopStart) {
374	<	bool update_nlist = fDecomp_->checkNeighborList();
375	<	if (update_nlist)
376	<	neighborMatW = fDecomp_->buildLayerBasedNeighborList();
377	<	}
373	>	void ForceManager::preCalculation() {
374	>	SimInfo::MoleculeIterator mi;
375	>	Molecule* mol;
376	>	Molecule::AtomIterator ai;
377	>	Atom* atom;
378	>	Molecule::RigidBodyIterator rbIter;
379	>	RigidBody* rb;
380	>	Molecule::CutoffGroupIterator ci;
381	>	CutoffGroup* cg;
382
383	<	int i;
592	<	#pragma omp parallel for num_threads(2) private(i)
593	<	for(i = 0; i < neighborMatW.size(); ++i)
594	<	for(vector<int>::iterator j = neighborMatW[i].begin(); j != neighborMatW[i].end(); ++j)
595	<	{
596	<	cg1 = i;
597	<	cg2 = *j;
383	>	// forces are zeroed here, before any are accumulated.
384
385	<	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
385	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
386	>	{
387	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai))
388	>	{
389	>	atom->zeroForcesAndTorques();
390	>	}
391
392	<	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
393	<	curSnapshot->wrapVector(d_grp);
394	<	rgrpsq = d_grp.lengthSquare();
392	>	//change the positions of atoms which belong to the rigidbodies
393	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter))
394	>	{
395	>	rb->zeroForcesAndTorques();
396	>	}
397
398	<	rCutSq = cuts.second;
398	>	if (info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms())
399	>	{
400	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
401	>	{
402	>	//calculate the center of mass of cutoff group
403	>	cg->updateCOM();
404	>	}
405	>	}
406	>	}
407
408	<	if (rgrpsq < rCutSq) {
409	<	idat.rcut = &cuts.first;
609	<	if (iLoop == PAIR_LOOP) {
610	<	vij = 0.0;
611	<	fij = V3Zero;
612	<	}
408	>	// Zero out the stress tensor
409	>	tau *= 0.0;
410
411	<	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
615	<	rgrp);
411	>	}
412
413	<	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
414	<	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
413	>	void ForceManager::shortRangeInteractions() {
414	>	Molecule* mol;
415	>	RigidBody* rb;
416	>	Bond* bond;
417	>	Bend* bend;
418	>	Torsion* torsion;
419	>	Inversion* inversion;
420	>	SimInfo::MoleculeIterator mi;
421	>	Molecule::RigidBodyIterator rbIter;
422	>	Molecule::BondIterator bondIter;
423	>	;
424	>	Molecule::BendIterator bendIter;
425	>	Molecule::TorsionIterator torsionIter;
426	>	Molecule::InversionIterator inversionIter;
427	>	RealType bondPotential = 0.0;
428	>	RealType bendPotential = 0.0;
429	>	RealType torsionPotential = 0.0;
430	>	RealType inversionPotential = 0.0;
431
432	<	for (vector<int>::iterator ia = atomListRow.begin();
433	<	ia != atomListRow.end(); ++ia) {
434	<	atom1 = (*ia);
432	>	//calculate short range interactions
433	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
434	>	{
435
436	<	for (vector<int>::iterator jb = atomListColumn.begin();
437	<	jb != atomListColumn.end(); ++jb) {
438	<	atom2 = (*jb);
436	>	//change the positions of atoms which belong to the rigidbodies
437	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter))
438	>	{
439	>	rb->updateAtoms();
440	>	}
441
442	<	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
443	<	vpair = 0.0;
444	<	workPot = 0.0;
445	<	f1 = V3Zero;
442	>	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter))
443	>	{
444	>	bond->calcForce();
445	>	bondPotential += bond->getPotential();
446	>	}
447
448	<	fDecomp_->fillInteractionData(idat, atom1, atom2);
448	>	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter))
449	>	{
450
451	<	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
452	<	vdwMult = vdwScale_[topoDist];
453	<	electroMult = electrostaticScale_[topoDist];
451	>	RealType angle;
452	>	bend->calcForce(angle);
453	>	RealType currBendPot = bend->getPotential();
454
455	<	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
456	<	idat.d = &d_grp;
457	<	idat.r2 = &rgrpsq;
458	<	cerr << "dgrp = " << d_grp << "\n";
459	<	} else {
460	<	d = fDecomp_->getInteratomicVector(atom1, atom2);
461	<	curSnapshot->wrapVector( d );
462	<	r2 = d.lengthSquare();
463	<	cerr << "datm = " << d<< "\n";
464	<	idat.d = &d;
465	<	idat.r2 = &r2;
466	<	}
455	>	bendPotential += bend->getPotential();
456	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
457	>	if (i == bendDataSets.end())
458	>	{
459	>	BendDataSet dataSet;
460	>	dataSet.prev.angle = dataSet.curr.angle = angle;
461	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
462	>	dataSet.deltaV = 0.0;
463	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
464	>	} else
465	>	{
466	>	i->second.prev.angle = i->second.curr.angle;
467	>	i->second.prev.potential = i->second.curr.potential;
468	>	i->second.curr.angle = angle;
469	>	i->second.curr.potential = currBendPot;
470	>	i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential);
471	>	}
472	>	}
473
474	<	cerr << "idat.d = " << *(idat.d) << "\n";
475	<	r = sqrt( *(idat.r2) );
476	<	idat.rij = &r;
474	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter))
475	>	{
476	>	RealType angle;
477	>	torsion->calcForce(angle);
478	>	RealType currTorsionPot = torsion->getPotential();
479	>	torsionPotential += torsion->getPotential();
480	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
481	>	if (i == torsionDataSets.end())
482	>	{
483	>	TorsionDataSet dataSet;
484	>	dataSet.prev.angle = dataSet.curr.angle = angle;
485	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
486	>	dataSet.deltaV = 0.0;
487	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
488	>	} else
489	>	{
490	>	i->second.prev.angle = i->second.curr.angle;
491	>	i->second.prev.potential = i->second.curr.potential;
492	>	i->second.curr.angle = angle;
493	>	i->second.curr.potential = currTorsionPot;
494	>	i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential);
495	>	}
496	>	}
497
498	<	if (iLoop == PREPAIR_LOOP) {
499	<	interactionMan_->doPrePair(idat);
500	<	} else {
501	<	interactionMan_->doPair(idat);
502	<	fDecomp_->unpackInteractionData(idat, atom1, atom2);
498	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(
499	>	inversionIter))
500	>	{
501	>	RealType angle;
502	>	inversion->calcForce(angle);
503	>	RealType currInversionPot = inversion->getPotential();
504	>	inversionPotential += inversion->getPotential();
505	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
506	>	if (i == inversionDataSets.end())
507	>	{
508	>	InversionDataSet dataSet;
509	>	dataSet.prev.angle = dataSet.curr.angle = angle;
510	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
511	>	dataSet.deltaV = 0.0;
512	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
513	>	} else
514	>	{
515	>	i->second.prev.angle = i->second.curr.angle;
516	>	i->second.prev.potential = i->second.curr.potential;
517	>	i->second.curr.angle = angle;
518	>	i->second.curr.potential = currInversionPot;
519	>	i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential);
520	>	}
521	>	}
522	>	}
523
524	<	cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n";
525	<	vij += vpair;
526	<	fij += f1;
527	<	tau -= outProduct( *(idat.d), f1);
528	<	}
529	<	}
530	<	}
531	<	}
524	>	RealType shortRangePotential = bondPotential + bendPotential + torsionPotential + inversionPotential;
525	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
526	>	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
527	>	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
528	>	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
529	>	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
530	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
531	>	}
532
533	<	if (iLoop == PAIR_LOOP) {
672	<	if (in_switching_region) {
673	<	swderiv = vij * dswdr / rgrp;
674	<	fg = swderiv * d_grp;
675	<	fij += fg;
533	>	void ForceManager::longRangeInteractionsRapaport() {
534
535	<	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
536	<	tau -= outProduct( *(idat.d), fg);
537	<	}
535	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
536	>	DataStorage* config = &(curSnapshot->atomData);
537	>	DataStorage* cgConfig = &(curSnapshot->cgData);
538
539	<	for (vector<int>::iterator ia = atomListRow.begin();
682	<	ia != atomListRow.end(); ++ia) {
683	<	atom1 = (*ia);
684	<	mf = fDecomp_->getMassFactorRow(atom1);
685	<	// fg is the force on atom ia due to cutoff group's
686	<	// presence in switching region
687	<	fg = swderiv * d_grp * mf;
688	<	fDecomp_->addForceToAtomRow(atom1, fg);
539	>	//calculate the center of mass of cutoff group
540
541	<	if (atomListRow.size() > 1) {
542	<	if (info_->usesAtomicVirial()) {
543	<	// find the distance between the atom
544	<	// and the center of the cutoff group:
694	<	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
695	<	tau -= outProduct(dag, fg);
696	<	}
697	<	}
698	<	}
699	<	for (vector<int>::iterator jb = atomListColumn.begin();
700	<	jb != atomListColumn.end(); ++jb) {
701	<	atom2 = (*jb);
702	<	mf = fDecomp_->getMassFactorColumn(atom2);
703	<	// fg is the force on atom jb due to cutoff group's
704	<	// presence in switching region
705	<	fg = -swderiv * d_grp * mf;
706	<	fDecomp_->addForceToAtomColumn(atom2, fg);
541	>	SimInfo::MoleculeIterator mi;
542	>	Molecule* mol;
543	>	Molecule::CutoffGroupIterator ci;
544	>	CutoffGroup* cg;
545
546	<	if (atomListColumn.size() > 1) {
547	<	if (info_->usesAtomicVirial()) {
548	<	// find the distance between the atom
549	<	// and the center of the cutoff group:
550	<	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
551	<	tau -= outProduct(dag, fg);
552	<	}
553	<	}
554	<	}
555	<	}
556	<	//if (!SIM_uses_AtomicVirial) {
557	<	//  tau -= outProduct(d_grp, fij);
558	<	//}
721	<	}
546	>	if (info_->getNCutoffGroups() > 0)
547	>	{
548	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
549	>	{
550	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
551	>	{
552	>	//                              cerr << "branch1\n";
553	>	//                              cerr << "globind = " << cg->getGlobalIndex() << ":" << __LINE__ << "\n";
554	>	cg->updateCOM();
555	>
556	>	//                              cerr << "gbI: " << cg->getGlobalIndex() << " locI: " << cg->getLocalIndex() << " x: "
557	>	//                                              << cgConfig->position[cg->getLocalIndex()].x() << " y: " << cgConfig->position[cg->getLocalIndex()].y()
558	>	//                                              << " z: " << cgConfig->position[cg->getLocalIndex()].z() << "\n";
559		}
560	<	}
560	>	}
561	>	} else
562	>	{
563	>	// center of mass of the group is the same as position of the atom
564	>	// if cutoff group does not exist
565	>	//              cerr << ":" << __LINE__ << "branch2\n";
566	>	cgConfig->position = config->position;
567	>	}
568
569	<	if (iLoop == PREPAIR_LOOP) {
570	<	if (info_->requiresPrepair()) {
569	>	fDecomp_->zeroWorkArrays();
570	>	fDecomp_->distributeData();
571
572	<	fDecomp_->collectIntermediateData();
572	>	int atom1, atom2, topoDist;
573	>	CutoffGroup *cg1;
574	>	Vector3d d_grp, dag, d;
575	>	RealType rgrpsq, rgrp, r2, r;
576	>	RealType electroMult, vdwMult;
577	>	RealType vij;
578	>	Vector3d fij, fg, f1;
579	>	tuple3<RealType, RealType, RealType> cuts;
580	>	RealType rCutSq;
581	>	bool in_switching_region;
582	>	RealType sw, dswdr, swderiv;
583	>	vector<int> atomListColumn, atomListRow, atomListLocal;
584	>	InteractionData idat;
585	>	SelfData sdat;
586	>	RealType mf;
587	>	RealType lrPot;
588	>	RealType vpair;
589	>	potVec longRangePotential(0.0);
590	>	potVec workPot(0.0);
591
592	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
731	<	fDecomp_->fillSelfData(sdat, atom1);
732	<	interactionMan_->doPreForce(sdat);
733	<	}
592	>	int loopStart, loopEnd;
593
594	<	fDecomp_->distributeIntermediateData();
594	>	idat.vdwMult = &vdwMult;
595	>	idat.electroMult = &electroMult;
596	>	idat.pot = &workPot;
597	>	sdat.pot = fDecomp_->getEmbeddingPotential();
598	>	idat.vpair = &vpair;
599	>	idat.f1 = &f1;
600	>	idat.sw = &sw;
601	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
602	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
603
604	<	}
605	<	}
604	>	loopEnd = PAIR_LOOP;
605	>	if (info_->requiresPrepair())
606	>	{
607	>	loopStart = PREPAIR_LOOP;
608	>	} else
609	>	{
610	>	loopStart = PAIR_LOOP;
611	>	}
612
613	<	}
613	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++)
614	>	{
615
616	<	fDecomp_->collectData();
616	>	if (iLoop == loopStart)
617	>	{
618	>	bool update_nlist = fDecomp_->checkNeighborList();
619	>	if (update_nlist)
620	>	neighborMatW = fDecomp_->buildLayerBasedNeighborList();
621	>	}
622
623	<	if (info_->requiresSelfCorrection()) {
623	>	//              printf("before omp loop\n");
624	>	//#pragma omp parallel for num_threads(3) default(none) shared(curSnapshot, idat, iLoop, sw, cerr) \
625	>	private(i, j, cg1, cg2, cuts, d_grp, rgrpsq, rCutSq, vij, fij, in_switching_region, rgrp, dswdr, atomListRow, atomListColumn, atom1, atom2, vpair, workPot, f1, topoDist, vdwMult, electroMult, d, r2, r, swderiv, fg, mf, dag)
626	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
627	>	{
628	>	for (cg1 = mol->beginCutoffGroup(ci); cg1 != NULL; cg1 = mol->nextCutoffGroup(ci))
629	>	{
630	>	//                      printf("Thread %d executes loop iteration %d\n", omp_get_thread_num(), i);
631	>	for (vector<CutoffGroup *>::iterator cg2 = neighborMatW[cg1->getGlobalIndex()].begin(); cg2 != neighborMatW[cg1->getGlobalIndex()].end(); ++cg2)
632	>	{
633
634	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
747	<	fDecomp_->fillSelfData(sdat, atom1);
748	<	interactionMan_->doSelfCorrection(sdat);
749	<	}
634	>	cuts = fDecomp_->getGroupCutoffs(cg1->getGlobalIndex(), (*cg2)->getGlobalIndex());
635
636	<	}
636	>	d_grp = fDecomp_->getIntergroupVector(cg1, (*cg2));
637	>	curSnapshot->wrapVector(d_grp);
638	>	rgrpsq = d_grp.lengthSquare();
639
640	<	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
754	<	*(fDecomp_->getPairwisePotential());
640	>	rCutSq = cuts.second;
641
642	<	lrPot = longRangePotential.sum();
642	>	if (rgrpsq < rCutSq)
643	>	{
644	>	idat.rcut = &cuts.first;
645	>	if (iLoop == PAIR_LOOP)
646	>	{
647	>	vij = 0.0;
648	>	fij = V3Zero;
649	>	}
650
651	<	//store the tau and long range potential
759	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
760	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
761	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
762	<	}
651	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, rgrp);
652
653	<	void ForceManager::longRangeInteractions() {
653	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1->getGlobalIndex());
654	>	atomListColumn = fDecomp_->getAtomsInGroupColumn((*cg2)->getGlobalIndex());
655
656	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
657	<	DataStorage* config = &(curSnapshot->atomData);
658	<	DataStorage* cgConfig = &(curSnapshot->cgData);
656	>	for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
657	>	{
658	>	atom1 = (*ia);
659
660	<	//calculate the center of mass of cutoff group
660	>	for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
661	>	{
662	>	atom2 = (*jb);
663
664	<	SimInfo::MoleculeIterator mi;
665	<	Molecule* mol;
666	<	Molecule::CutoffGroupIterator ci;
667	<	CutoffGroup* cg;
664	>	if (!fDecomp_->skipAtomPair(atom1, atom2))
665	>	{
666	>	vpair = 0.0;
667	>	workPot = 0.0;
668	>	f1 = V3Zero;
669
670	<	if(info_->getNCutoffGroups() > 0){
778	<	for (mol = info_->beginMolecule(mi); mol != NULL;
779	<	mol = info_->nextMolecule(mi)) {
780	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
781	<	cg = mol->nextCutoffGroup(ci)) {
782	<	cerr << "branch1\n";
783	<	cerr << "globind = " << cg->getGlobalIndex() << "\n";
784	<	cg->updateCOM();
785	<	}
786	<	}
787	<	} else {
788	<	// center of mass of the group is the same as position of the atom
789	<	// if cutoff group does not exist
790	<	cerr << "branch2\n";
791	<	cgConfig->position = config->position;
792	<	}
670	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
671
672	<	fDecomp_->zeroWorkArrays();
673	<	fDecomp_->distributeData();
674	<
797	<	int cg1, cg2, atom1, atom2, topoDist;
798	<	Vector3d d_grp, dag, d;
799	<	RealType rgrpsq, rgrp, r2, r;
800	<	RealType electroMult, vdwMult;
801	<	RealType vij;
802	<	Vector3d fij, fg, f1;
803	<	tuple3<RealType, RealType, RealType> cuts;
804	<	RealType rCutSq;
805	<	bool in_switching_region;
806	<	RealType sw, dswdr, swderiv;
807	<	vector<int> atomListColumn, atomListRow, atomListLocal;
808	<	InteractionData idat;
809	<	SelfData sdat;
810	<	RealType mf;
811	<	RealType lrPot;
812	<	RealType vpair;
813	<	potVec longRangePotential(0.0);
814	<	potVec workPot(0.0);
672	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
673	>	vdwMult = vdwScale_[topoDist];
674	>	electroMult = electrostaticScale_[topoDist];
675
676	<	int loopStart, loopEnd;
676	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1)
677	>	{
678	>	idat.d = &d_grp;
679	>	idat.r2 = &rgrpsq;
680	>	//                                                                              cerr << "dgrp = " << d_grp << ":" << __LINE__ << "\n";
681	>	} else
682	>	{
683	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
684	>	curSnapshot->wrapVector(d);
685	>	r2 = d.lengthSquare();
686	>	//                                                                              cerr << "datm = " << d << ":" << __LINE__ << "\n";
687	>	idat.d = &d;
688	>	idat.r2 = &r2;
689	>	}
690
691	<	idat.vdwMult = &vdwMult;
692	<	idat.electroMult = &electroMult;
693	<	idat.pot = &workPot;
694	<	sdat.pot = fDecomp_->getEmbeddingPotential();
822	<	idat.vpair = &vpair;
823	<	idat.f1 = &f1;
824	<	idat.sw = &sw;
825	<	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
826	<	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
827	<
828	<	loopEnd = PAIR_LOOP;
829	<	if (info_->requiresPrepair() ) {
830	<	loopStart = PREPAIR_LOOP;
831	<	} else {
832	<	loopStart = PAIR_LOOP;
833	<	}
834	<
835	<	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
836	<
837	<	if (iLoop == loopStart) {
838	<	bool update_nlist = fDecomp_->checkNeighborList();
839	<	if (update_nlist)
840	<	neighborList = fDecomp_->buildNeighborList();
691	>	//                                                                      cerr << "idat.d = " << *(idat.d) << ":" << __LINE__ << "\n";
692	>	r = sqrt(*(idat.r2));
693	>	idat.rij = &r;
694	>	//                                                                      cerr << "idat.rij = " << *(idat.rij) << "\n";
695
696	<	}
697	<
698	<	for (vector<pair<int, int> >::iterator it = neighborList.begin();
699	<	it != neighborList.end(); ++it)
700	<	{
701	<	cg1 = (*it).first;
702	<	cg2 = (*it).second;
849	<
850	<	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
696	>	if (iLoop == PREPAIR_LOOP)
697	>	{
698	>	interactionMan_->doPrePair(idat);
699	>	} else
700	>	{
701	>	interactionMan_->doPair(idat);
702	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
703
704	<	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
705	<	curSnapshot->wrapVector(d_grp);
706	<	rgrpsq = d_grp.lengthSquare();
704	>	//                                                                              cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << ":" << __LINE__ << "\n";
705	>	vij += vpair;
706	>	fij += f1;
707	>	tau -= outProduct(*(idat.d), f1);
708	>	}
709	>	}
710	>	}
711	>	}
712
713	<	rCutSq = cuts.second;
713	>	if (iLoop == PAIR_LOOP)
714	>	{
715	>	if (in_switching_region)
716	>	{
717	>	swderiv = vij * dswdr / rgrp;
718	>	fg = swderiv * d_grp;
719	>	fij += fg;
720
721	<	if (rgrpsq < rCutSq) {
722	<	idat.rcut = &cuts.first;
723	<	if (iLoop == PAIR_LOOP) {
724	<	vij = 0.0;
862	<	fij = V3Zero;
863	<	}
864	<
865	<	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
866	<	rgrp);
867	<
868	<	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
869	<	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
721	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1)
722	>	{
723	>	tau -= outProduct(*(idat.d), fg);
724	>	}
725
726	<	for (vector<int>::iterator ia = atomListRow.begin();
727	<	ia != atomListRow.end(); ++ia) {
728	<	atom1 = (*ia);
729	<
730	<	for (vector<int>::iterator jb = atomListColumn.begin();
731	<	jb != atomListColumn.end(); ++jb) {
732	<	atom2 = (*jb);
726	>	for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
727	>	{
728	>	atom1 = (*ia);
729	>	mf = fDecomp_->getMassFactorRow(atom1);
730	>	// fg is the force on atom ia due to cutoff group's
731	>	// presence in switching region
732	>	fg = swderiv * d_grp * mf;
733	>	fDecomp_->addForceToAtomRow(atom1, fg);
734
735	<	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
736	<	vpair = 0.0;
737	<	workPot = 0.0;
738	<	f1 = V3Zero;
735	>	if (atomListRow.size() > 1)
736	>	{
737	>	if (info_->usesAtomicVirial())
738	>	{
739	>	// find the distance between the atom
740	>	// and the center of the cutoff group:
741	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1->getGlobalIndex());
742	>	tau -= outProduct(dag, fg);
743	>	}
744	>	}
745	>	}
746	>	for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
747	>	{
748	>	atom2 = (*jb);
749	>	mf = fDecomp_->getMassFactorColumn(atom2);
750	>	// fg is the force on atom jb due to cutoff group's
751	>	// presence in switching region
752	>	fg = -swderiv * d_grp * mf;
753	>	fDecomp_->addForceToAtomColumn(atom2, fg);
754
755	<	fDecomp_->fillInteractionData(idat, atom1, atom2);
756	<
757	<	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
758	<	vdwMult = vdwScale_[topoDist];
759	<	electroMult = electrostaticScale_[topoDist];
755	>	if (atomListColumn.size() > 1)
756	>	{
757	>	if (info_->usesAtomicVirial())
758	>	{
759	>	// find the distance between the atom
760	>	// and the center of the cutoff group:
761	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, (*cg2)->getGlobalIndex());
762	>	tau -= outProduct(dag, fg);
763	>	}
764	>	}
765	>	}
766	>	}
767	>	//if (!SIM_uses_AtomicVirial) {
768	>	//  tau -= outProduct(d_grp, fij);
769	>	//}
770	>	}
771	>	}
772	>	}
773	>	}
774	>	}// END: omp for loop
775	>	//              printf("after omp loop\n");
776
777	<	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
778	<	idat.d = &d_grp;
779	<	idat.r2 = &rgrpsq;
780	<	cerr << "dgrp = " << d_grp << "\n";
894	<	} else {
895	<	d = fDecomp_->getInteratomicVector(atom1, atom2);
896	<	curSnapshot->wrapVector( d );
897	<	r2 = d.lengthSquare();
898	<	cerr << "datm = " << d<< "\n";
899	<	idat.d = &d;
900	<	idat.r2 = &r2;
901	<	}
902	<
903	<	cerr << "idat.d = " << *(idat.d) << "\n";
904	<	r = sqrt( *(idat.r2) );
905	<	idat.rij = &r;
906	<
907	<	if (iLoop == PREPAIR_LOOP) {
908	<	interactionMan_->doPrePair(idat);
909	<	} else {
910	<	interactionMan_->doPair(idat);
911	<	fDecomp_->unpackInteractionData(idat, atom1, atom2);
777	>	if (iLoop == PREPAIR_LOOP)
778	>	{
779	>	if (info_->requiresPrepair())
780	>	{
781
782	<	cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n";
914	<	vij += vpair;
915	<	fij += f1;
916	<	tau -= outProduct( *(idat.d), f1);
917	<	}
918	<	}
919	<	}
920	<	}
782	>	fDecomp_->collectIntermediateData();
783
784	<	if (iLoop == PAIR_LOOP) {
785	<	if (in_switching_region) {
786	<	swderiv = vij * dswdr / rgrp;
787	<	fg = swderiv * d_grp;
788	<	fij += fg;
784	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
785	>	{
786	>	fDecomp_->fillSelfData(sdat, atom1);
787	>	interactionMan_->doPreForce(sdat);
788	>	}
789
790	<	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
929	<	tau -= outProduct( *(idat.d), fg);
930	<	}
931	<
932	<	for (vector<int>::iterator ia = atomListRow.begin();
933	<	ia != atomListRow.end(); ++ia) {
934	<	atom1 = (*ia);
935	<	mf = fDecomp_->getMassFactorRow(atom1);
936	<	// fg is the force on atom ia due to cutoff group's
937	<	// presence in switching region
938	<	fg = swderiv * d_grp * mf;
939	<	fDecomp_->addForceToAtomRow(atom1, fg);
790	>	fDecomp_->distributeIntermediateData();
791
792	<	if (atomListRow.size() > 1) {
793	<	if (info_->usesAtomicVirial()) {
794	<	// find the distance between the atom
944	<	// and the center of the cutoff group:
945	<	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
946	<	tau -= outProduct(dag, fg);
947	<	}
948	<	}
949	<	}
950	<	for (vector<int>::iterator jb = atomListColumn.begin();
951	<	jb != atomListColumn.end(); ++jb) {
952	<	atom2 = (*jb);
953	<	mf = fDecomp_->getMassFactorColumn(atom2);
954	<	// fg is the force on atom jb due to cutoff group's
955	<	// presence in switching region
956	<	fg = -swderiv * d_grp * mf;
957	<	fDecomp_->addForceToAtomColumn(atom2, fg);
792	>	}
793	>	}
794	>	}
795
796	<	if (atomListColumn.size() > 1) {
960	<	if (info_->usesAtomicVirial()) {
961	<	// find the distance between the atom
962	<	// and the center of the cutoff group:
963	<	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
964	<	tau -= outProduct(dag, fg);
965	<	}
966	<	}
967	<	}
968	<	}
969	<	//if (!SIM_uses_AtomicVirial) {
970	<	//  tau -= outProduct(d_grp, fij);
971	<	//}
972	<	}
973	<	}
974	<	}
796	>	fDecomp_->collectData();
797
798	<	if (iLoop == PREPAIR_LOOP) {
799	<	if (info_->requiresPrepair()) {
798	>	if (info_->requiresSelfCorrection())
799	>	{
800
801	<	fDecomp_->collectIntermediateData();
801	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
802	>	{
803	>	fDecomp_->fillSelfData(sdat, atom1);
804	>	interactionMan_->doSelfCorrection(sdat);
805	>	}
806
807	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
982	<	fDecomp_->fillSelfData(sdat, atom1);
983	<	interactionMan_->doPreForce(sdat);
984	<	}
807	>	}
808
809	<	fDecomp_->distributeIntermediateData();
809	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) + *(fDecomp_->getPairwisePotential());
810
811	<	}
989	<	}
811	>	lrPot = longRangePotential.sum();
812
813	<	}
814	<
815	<	fDecomp_->collectData();
816	<
817	<	if (info_->requiresSelfCorrection()) {
813	>	//store the tau and long range potential
814	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
815	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
816	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
817	>	}
818
819	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
998	<	fDecomp_->fillSelfData(sdat, atom1);
999	<	interactionMan_->doSelfCorrection(sdat);
1000	<	}
819	>	void ForceManager::longRangeInteractions() {
820
821	<	}
821	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
822	>	DataStorage* config = &(curSnapshot->atomData);
823	>	DataStorage* cgConfig = &(curSnapshot->cgData);
824
825	<	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
1005	<	*(fDecomp_->getPairwisePotential());
825	>	//calculate the center of mass of cutoff group
826
827	<	lrPot = longRangePotential.sum();
827	>	SimInfo::MoleculeIterator mi;
828	>	Molecule* mol;
829	>	Molecule::CutoffGroupIterator ci;
830	>	CutoffGroup* cg;
831
832	<	//store the tau and long range potential
833	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
834	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
835	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
836	<	}
832	>	if (info_->getNCutoffGroups() > 0)
833	>	{
834	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
835	>	{
836	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
837	>	{
838	>	cerr << "branch1\n";
839	>	cerr << "globind = " << cg->getGlobalIndex() << "\n";
840	>	cg->updateCOM();
841	>	}
842	>	}
843	>	} else
844	>	{
845	>	// center of mass of the group is the same as position of the atom
846	>	// if cutoff group does not exist
847	>	cerr << "branch2\n";
848	>	cgConfig->position = config->position;
849	>	}
850
851	<
852	<	void ForceManager::postCalculation() {
853	<	SimInfo::MoleculeIterator mi;
854	<	Molecule* mol;
855	<	Molecule::RigidBodyIterator rbIter;
856	<	RigidBody* rb;
857	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
858	<
859	<	// collect the atomic forces onto rigid bodies
860	<
861	<	for (mol = info_->beginMolecule(mi); mol != NULL;
862	<	mol = info_->nextMolecule(mi)) {
863	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
864	<	rb = mol->nextRigidBody(rbIter)) {
865	<	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
866	<	tau += rbTau;
867	<	}
868	<	}
869	<
851	>	fDecomp_->zeroWorkArrays();
852	>	fDecomp_->distributeData();
853	>
854	>	int cg1, cg2, atom1, atom2, topoDist;
855	>	Vector3d d_grp, dag, d;
856	>	RealType rgrpsq, rgrp, r2, r;
857	>	RealType electroMult, vdwMult;
858	>	RealType vij;
859	>	Vector3d fij, fg, f1;
860	>	tuple3<RealType, RealType, RealType> cuts;
861	>	RealType rCutSq;
862	>	bool in_switching_region;
863	>	RealType sw, dswdr, swderiv;
864	>	vector<int> atomListColumn, atomListRow, atomListLocal;
865	>	InteractionData idat;
866	>	SelfData sdat;
867	>	RealType mf;
868	>	RealType lrPot;
869	>	RealType vpair;
870	>	potVec longRangePotential(0.0);
871	>	potVec workPot(0.0);
872	>
873	>	int loopStart, loopEnd;
874	>
875	>	idat.vdwMult = &vdwMult;
876	>	idat.electroMult = &electroMult;
877	>	idat.pot = &workPot;
878	>	sdat.pot = fDecomp_->getEmbeddingPotential();
879	>	idat.vpair = &vpair;
880	>	idat.f1 = &f1;
881	>	idat.sw = &sw;
882	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
883	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
884	>
885	>	loopEnd = PAIR_LOOP;
886	>	if (info_->requiresPrepair())
887	>	{
888	>	loopStart = PREPAIR_LOOP;
889	>	} else
890	>	{
891	>	loopStart = PAIR_LOOP;
892	>	}
893	>
894	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++)
895	>	{
896	>
897	>	if (iLoop == loopStart)
898	>	{
899	>	bool update_nlist = fDecomp_->checkNeighborList();
900	>	if (update_nlist)
901	>	neighborList = fDecomp_->buildNeighborList();
902	>
903	>	}
904	>
905	>	for (vector<pair<int, int> >::iterator it = neighborList.begin(); it != neighborList.end(); ++it)
906	>	{
907	>	cg1 = (*it).first;
908	>	cg2 = (*it).second;
909	>
910	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
911	>
912	>	d_grp = fDecomp_->getIntergroupVector(cg1, cg2);
913	>	curSnapshot->wrapVector(d_grp);
914	>	rgrpsq = d_grp.lengthSquare();
915	>
916	>	rCutSq = cuts.second;
917	>
918	>	if (rgrpsq < rCutSq)
919	>	{
920	>	idat.rcut = &cuts.first;
921	>	if (iLoop == PAIR_LOOP)
922	>	{
923	>	vij = 0.0;
924	>	fij = V3Zero;
925	>	}
926	>
927	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, rgrp);
928	>
929	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
930	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
931	>
932	>	for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
933	>	{
934	>	atom1 = (*ia);
935	>
936	>	for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
937	>	{
938	>	atom2 = (*jb);
939	>
940	>	if (!fDecomp_->skipAtomPair(atom1, atom2))
941	>	{
942	>	vpair = 0.0;
943	>	workPot = 0.0;
944	>	f1 = V3Zero;
945	>
946	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
947	>
948	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
949	>	vdwMult = vdwScale_[topoDist];
950	>	electroMult = electrostaticScale_[topoDist];
951	>
952	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1)
953	>	{
954	>	idat.d = &d_grp;
955	>	idat.r2 = &rgrpsq;
956	>	cerr << "dgrp = " << d_grp << "\n";
957	>	} else
958	>	{
959	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
960	>	curSnapshot->wrapVector(d);
961	>	r2 = d.lengthSquare();
962	>	cerr << "datm = " << d << "\n";
963	>	idat.d = &d;
964	>	idat.r2 = &r2;
965	>	}
966	>
967	>	cerr << "idat.d = " << *(idat.d) << "\n";
968	>	r = sqrt(*(idat.r2));
969	>	idat.rij = &r;
970	>
971	>	if (iLoop == PREPAIR_LOOP)
972	>	{
973	>	interactionMan_->doPrePair(idat);
974	>	} else
975	>	{
976	>	interactionMan_->doPair(idat);
977	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
978	>
979	>	cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n";
980	>	vij += vpair;
981	>	fij += f1;
982	>	tau -= outProduct(*(idat.d), f1);
983	>	}
984	>	}
985	>	}
986	>	}
987	>
988	>	if (iLoop == PAIR_LOOP)
989	>	{
990	>	if (in_switching_region)
991	>	{
992	>	swderiv = vij * dswdr / rgrp;
993	>	fg = swderiv * d_grp;
994	>	fij += fg;
995	>
996	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1)
997	>	{
998	>	tau -= outProduct(*(idat.d), fg);
999	>	}
1000	>
1001	>	for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
1002	>	{
1003	>	atom1 = (*ia);
1004	>	mf = fDecomp_->getMassFactorRow(atom1);
1005	>	// fg is the force on atom ia due to cutoff group's
1006	>	// presence in switching region
1007	>	fg = swderiv * d_grp * mf;
1008	>	fDecomp_->addForceToAtomRow(atom1, fg);
1009	>
1010	>	if (atomListRow.size() > 1)
1011	>	{
1012	>	if (info_->usesAtomicVirial())
1013	>	{
1014	>	// find the distance between the atom
1015	>	// and the center of the cutoff group:
1016	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
1017	>	tau -= outProduct(dag, fg);
1018	>	}
1019	>	}
1020	>	}
1021	>	for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
1022	>	{
1023	>	atom2 = (*jb);
1024	>	mf = fDecomp_->getMassFactorColumn(atom2);
1025	>	// fg is the force on atom jb due to cutoff group's
1026	>	// presence in switching region
1027	>	fg = -swderiv * d_grp * mf;
1028	>	fDecomp_->addForceToAtomColumn(atom2, fg);
1029	>
1030	>	if (atomListColumn.size() > 1)
1031	>	{
1032	>	if (info_->usesAtomicVirial())
1033	>	{
1034	>	// find the distance between the atom
1035	>	// and the center of the cutoff group:
1036	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
1037	>	tau -= outProduct(dag, fg);
1038	>	}
1039	>	}
1040	>	}
1041	>	}
1042	>	//if (!SIM_uses_AtomicVirial) {
1043	>	//  tau -= outProduct(d_grp, fij);
1044	>	//}
1045	>	}
1046	>	}
1047	>	}
1048	>
1049	>	if (iLoop == PREPAIR_LOOP)
1050	>	{
1051	>	if (info_->requiresPrepair())
1052	>	{
1053	>
1054	>	fDecomp_->collectIntermediateData();
1055	>
1056	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
1057	>	{
1058	>	fDecomp_->fillSelfData(sdat, atom1);
1059	>	interactionMan_->doPreForce(sdat);
1060	>	}
1061	>
1062	>	fDecomp_->distributeIntermediateData();
1063	>
1064	>	}
1065	>	}
1066	>
1067	>	}
1068	>
1069	>	fDecomp_->collectData();
1070	>
1071	>	if (info_->requiresSelfCorrection())
1072	>	{
1073	>
1074	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
1075	>	{
1076	>	fDecomp_->fillSelfData(sdat, atom1);
1077	>	interactionMan_->doSelfCorrection(sdat);
1078	>	}
1079	>
1080	>	}
1081	>
1082	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) + *(fDecomp_->getPairwisePotential());
1083	>
1084	>	lrPot = longRangePotential.sum();
1085	>
1086	>	//store the tau and long range potential
1087	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
1088	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
1089	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
1090	>	}
1091	>
1092	>	void ForceManager::postCalculation() {
1093	>	SimInfo::MoleculeIterator mi;
1094	>	Molecule* mol;
1095	>	Molecule::RigidBodyIterator rbIter;
1096	>	RigidBody* rb;
1097	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
1098	>
1099	>	// collect the atomic forces onto rigid bodies
1100	>
1101	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1102	>	{
1103	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter))
1104	>	{
1105	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
1106	>	tau += rbTau;
1107	>	}
1108	>	}
1109	>
1110		#ifdef IS_MPI
1111	<	Mat3x3d tmpTau(tau);
1112	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
1113	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1111	>	Mat3x3d tmpTau(tau);
1112	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
1113	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1114		#endif
1115	<	curSnapshot->statData.setTau(tau);
1116	<	}
1115	>	curSnapshot->statData.setTau(tau);
1116	>	}
1117
1118		} //end namespace OpenMD

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